Cephalopod DNA/Molecular/Genetic Studies/Health

This is a review of the current status of ceph molecular data collection. @gjbarord is currently doing DNA work with the nautilus and hopefully will post where the information can be accessed once it is stored.

Abstract
The first DNA sequence of a cephalopod was published in 1983 and the first molecular paper focusing on cephalopods was published in 1994. In this review we trace progress in the field. We examine the placement of Cephalopoda with respect to other molluscan classes and we examine relationships within Cephalopoda. We provide a summary tree of the relationships between cephalopod orders and we examine relationships of taxa within each of these orders. Although much knowledge has been gained over the past 20 years, deeper-level relationships are still not well understood and there is still much scope for further research in this field. Genomic studies are likely to contribute significantly to our knowledge in the future.

Abstract
Cranchiids were the most diverse squid family collected during the first southern MAR-ECO expedition in late 2009, with nine taxa identified to species. A total of 45 young specimens were collected (mantle length 7.4–59.2 mm), allowing a survey of early ontogenetic tentacular morphology in cranchiids using scanning electron micrographs. Paralarval tentacular sucker morphology appeared similar among species within the same subfamily: in the Cranchiinae, the paralarval suckers possess relatively large, narrowly polygonal or ovoid-faced pegs in the innermost ring around the aperture, and the infundibular ring lacks the dentition observed in most taoniin genera. Hook development in Galiteuthis armata appears to vary widely among small individuals. Tissue samples were also collected from five genera (Cranchia, Galiteuthis, Helicocranchia, Leachia and Teuthowenia); phylogenetic trees (maximum-likelihood and Bayesian methods) built using these cytochrome oxidase subunit I sequences and others available from GenBank show some support for the subfamilies Cranchiinae and Taoniinae, and that within the latter, the hooked taxa group together. It is hoped that reporting this opportunistic systematic and genetic information may be of eventual assistance in helping to resolve this most problematic of squid families.

Abstract
Cytochrome c oxidase subunit-1 (CO1) gene sequence of enope squid Abralia andamanica sampled from Andaman Sea was compared with the CO1 gene sequence of A. andamanica from China Sea. Assessment of CO1 nucleotide and protein sequence of enope squid Abralia andamanica from Andaman Sea and China Sea revealed that with respect to CO1 sequence genetic divergence exist between the two enope squids. A. andamanica inhabiting Andaman Sea exhibited more affinity towards A. veranyi than to its counterpart from China Sea. Pairwise distance calculated based on Kimura 2-parameter (K2P) model for the enope squids from Andaman Sea and China Sea was found to be almost half of the mean pairwise distance determined for order Teuthida indicating high genetic variation among the two enope squids with regard to CO1 gene. Phylogenetic analysis of the CO1 nucleotide sequence of A. andamanica was performed to determine its relationship with other squids belonging to the order Teuthida. A. andamanica aligned along with the clade formed by family Enoploteuthidae. Sixteen families of order Teuthida were considered for phylogenetic analysis, overlap was observed three families. The study endorses the proficiency of CO1 based DNA barcoding in determining the phylogeny and genetic divergence of a species.

Bolstad, K. S., Braid, H. E., & McBride, P. D. Molecular phylogenetic analysis of the squid family Mastigoteuthidae (Mollusca, Cephalopoda) based on three mitochondrial genes [2014].
Abstract:
Mastigoteuthid squids are ecologically important, being prey to many apex predators, yet the diversity and systematics of the family remain poorly understood. Delicate by nature, they are often damaged during capture; there is a need to accurately identify incomplete mastigoteuthid specimens from collections and stomach contents. This study aimed to test a morphological hypothesis for the division of the genera Mastigoteuthis� (Mt.), Idioteuthis, Mastigopsis (Mp.), Echinoteuthis, and Magnoteuthis (Mg.) and to assess the utility of DNA barcodes to discriminate species. Three mitochondrial genes (16S rRNA, 12S rRNA, and cytochrome c oxidase subunit I) were analysed for eight different species, representing the largest phylogenetic assessment of the family to date. Evidence was found for a potentially new species in New Zealand that has been previously misidentified as the morphologically similar species Mg. magna. Each species analysed herein exhibited unique mitochondrial DNA haplotypes for all loci, and the morphological distinction between the five proposed genera was strongly supported using a combined Bayesian and maximum-likelihood phylogenies. Of the three loci examined, the DNA barcode region shows the greatest divergence between species and should be used in future systematic work on the Mastigoteuthidae.

Abstract
Population substructure of Sepia officinalis sampled along the Tunisian coastline was studied. We have scored the genetic variation of the mitochondrial gene cytochrome oxidase 1. A total of 20 specimens from four sampling sites were analysed and revealed 12 different haplotypes. Haplotype diversity showed a decreasing north to south gradient which may be explained by the hydrogeography of the study area. The overall estimate of genetic divergence (FST) revealed significant genetic differentiation between the pair-wise population comparisons supported by the AMOVA analysis which reveals significant genetic divergence. Finally, populations showed an excess of rare haplotypes. The mismatch distribution and several population genetic statistics indicate that the excess of rare variants is due to a recent expansion for Djerba and Kelibia populations. For Rades and Bizerte populations a constant population size was detected. These findings are important for fisheries management to preserve this marine resource for long-term utilization.

Abstract
Cephalopod mollusks possess a number of anatomical traits that often parallel vertebrates in morphological complexity, including a centralized nervous system with sophisticated cognitive functionality. Very little is known about the genetic mechanisms underlying patterning of the cephalopod embryo to arrive at this anatomical structure. Homeodomain (HD) genes are transcription factors that regulate transcription of downstream genes through DNA binding, and as such are integral parts of gene regulatory networks controlling the specification and patterning of body parts across lineages. We have used a degenerate primer strategy to isolate homeobox genes active during late-organogenesis from the European cuttlefish Sepia officinalis. With this approach we have isolated fourteen HD gene fragments and examine the expression profiles of five of these genes during late stage (E24-28) embryonic development (Sof-Gbx, Sof-Hox3, Sof-Arx, Sof-Lhx3/4, Sof-Vsx). All five genes are expressed within the developing central nervous system in spatially restricted and largely non-overlapping domains. Our data provide a first glimpse into the diversity of HD genes in one of the largest, yet least studied, metazoan clades and illustrate how HD gene expression patterns reflect the functional partitioning of the cephalopod brain.

Abstract
The molluscan neuro-muscular system shows extreme diversity. Cephalopods present an original body plan, a derived neuro-muscular complex and a development with drastic changes in the antero-posterior/dorso-ventral orientation. How it took place during evolution is an unresolved question that can be approached by the study of developmental genes. Studying the expression of conserved transcription factors (Pax and NK families, otx, apt) and morphogen (hedgehog) during development is a good test of the conservation of their functions. We underline here unexpected expression patterns during cephalopod development, and we aim to suggest that these patterns may be, at least partly, in relation to morphological novelties in this clade.

Tel Aviv University researcher discovers that squid recode their genetic make-up on-the-fly to adjust to their surroundings
American Friends of Tel Aviv University 2015 news article

The principle of adaptation -- the gradual modification of a species' structures and features -- is one of the pillars of evolution. While there exists ample evidence to support the slow, ongoing process that alters the genetic makeup of a species, scientists could only suspect that there were also organisms capable of transforming themselves ad hoc to adjust to changing conditions.

Now a new study published in eLife by Dr. Eli Eisenberg of Tel Aviv University's Department of Physics and Sagol School of Neuroscience, in collaboration with Dr. Joshua J. Rosenthal of the University of Puerto Rico, showcases the first example of an animal editing its own genetic makeup on-the-fly to modify most of its proteins, enabling adjustments to its immediate surroundings. The research, conducted in part by TAU graduate student Shahar Alon, explored RNA editing in the Doryteuthis pealieii squid.

"We have demonstrated that RNA editing is a major player in genetic information processing rather than an exception to the rule," said Dr. Eisenberg. "By showing that the squid's RNA-editing dramatically reshaped its entire proteome -- the entire set of proteins expressed by a genome, cell, tissue, or organism at a certain time -- we proved that an organism's self-editing of mRNA is a critical evolutionary and adaptive force." This demonstration, he said, may have implications for human diseases as well.

Using the genetic red pencil

RNA is a copy of the genetic code that is translated into protein. But the RNA "transcript" can be edited before being translated into protein, paving the way for different versions of proteins. Abnormal RNA editing in humans has been observed in patients with neurological diseases. The changing physiological appearance of squid and octopuses over their lifetime and across different habitats has suggested extensive recoding might occur in these species. However, this could never be confirmed, as their genomes (and those of most species) have never been sequenced.

For the purpose of the new study, the researchers extracted both DNA and RNA from squid. Harnessing DNA sequencing and computational analyses at TAU, the team compared the RNA and DNA sequences to observe differences. The sequences in which the RNA and DNA did not match up were identified as "edited."

"It was astonishing to find that 60 percent of the squid RNA transcripts were edited. The fruit fly, for the sake of comparison, is thought to edit only 3% of its makeup," said Dr. Eisenberg. "Why do squid edit to such an extent? One theory is that they have an extremely complex nervous system, exhibiting behavioral sophistication unusual for invertebrates. They may also utilize this mechanism to respond to changing temperatures and other environmental parameters."

"Misfolding" the proteins

The researchers hope to use this approach to identify recoding sites in other organisms whose genomes have not been sequenced.

"We would like to understand better how prevalent this phenomenon is in the animal world. How is it regulated? How is it exploited to confer adaptability?" said Dr. Eisenberg. "There may be implications for us as well. Human diseases are often the result of 'misfolded' proteins, which often become toxic. Therefore the question of treating the misfolded proteins, likely to be generated by such an extensive recoding as exhibited in the squid cells, is very important for future therapeutic approaches. Does the squid have some mechanism we can learn from?"

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The researchers recently received an Israel-U.S. Binational Science Foundation grant to explore the subject of genetic editing in octopuses.

American Friends of Tel Aviv University supports Israel's most influential, most comprehensive and most sought-after center of higher learning, Tel Aviv University (TAU). US News & World Report's Best Global Universities Rankings rate TAU as #148 in the world, and the Times Higher Education World University Rankings rank TAU Israel's top university. It is one of a handful of elite international universities rated as the best producers of successful startups, and TAU alumni rank #9 in the world for the amount of American venture capital they attract.

A leader in the pan-disciplinary approach to education, TAU is internationally recognized for the scope and groundbreaking nature of its research and scholarship -- attracting world-class faculty and consistently producing cutting-edge work with profound implications for the future

Coleoid cephalopods (octopus, squid and cuttlefish) are active, resourceful predators with a rich behavioural repertoire1. They have the largest nervous systems among the invertebrates2 and present other striking morphological innovations including camera-like eyes, prehensile arms, a highly derived early embryogenesis and a remarkably sophisticated adaptive colouration system1, 3. To investigate the molecular bases of cephalopod brain and body innovations, we sequenced the genome and multiple transcriptomes of the California two-spot octopus, Octopus bimaculoides. We found no evidence for hypothesized whole-genome duplications in the octopus lineage4, 5, 6. The core developmental and neuronal gene repertoire of the octopus is broadly similar to that found across invertebrate bilaterians, except for massive expansions in two gene families previously thought to be uniquely enlarged in vertebrates: the protocadherins, which regulate neuronal development, and the C2H2 superfamily of zinc-finger transcription factors. Extensive messenger RNA editing generates transcript and protein diversity in genes involved in neural excitability, as previously described7, as well as in genes participating in a broad range of other cellular functions. We identified hundreds of cephalopod-specific genes, many of which showed elevated expression levels in such specialized structures as the skin, the suckers and the nervous system. Finally, we found evidence for large-scale genomic rearrangements that are closely associated with transposable element expansions. Our analysis suggests that substantial expansion of a handful of gene families, along with extensive remodelling of genome linkage and repetitive content, played a critical role in the evolution of cephalopod morphological innovations, including their large and complex nervous systems. ...

The ‘Mimic Octopus’Thaumoctopus mimicus Norman & Hochberg, 2005 exhibits a conspicuous primary defence mechanism (high-contrast colour pattern during ‘flatfish swimming’) that may involve facultative imperfect mimicry of conspicuous and/or inconspicuous models, both toxic and non-toxic (Soleidae and Bothidae). Here, we examine relationships between behavioural and morphological elements of conspicuous flatfish swimming in extant octopodids (Cephalopoda: Octopodidae), and reconstructed ancestral states, to examine potential influences on the evolution of this rare defence mechanism. We address the order of trait distribution to explore whether conspicuous flatfish swimming may be an exaptation that usurps a previously evolved form of locomotion for a new purpose. Contrary to our predictions, based on the relationships we examined, flatfish swimming appears to have evolved concurrently with extremely long arms, in a clade of sand-dwelling species. The conspicuous body colour pattern displayed by swimming T. mimicus may represent a secondary adaptation potentially allowing for mimicry of a toxic sole, improved disruptive coloration, and/or aposematic coloration.

If you have a free account with Research gate, you can download the full pdf- it has pics of the mimic's relatives:

Not to freak you out or anything, but scientists have just revealed that octopuses are so weird they’re basically aliens.

The first full genome sequence shows of that octopuses (NOT octopi) are totally different from all other animals – and their genome shows a striking level of complexity with 33,000 protein-coding genes identified, more than in a human.

Bullshit.

As I said earlier, the study is open access. Read it. If you can’t understand the big words and the details, then you shouldn’t be writing news stories on science.

The study says exactly the opposite. It shows that octopuses use genes shared with vertebrates — the common metazoan toolbox. They have amplified genes used by other earthly animal life in unique ways, but protocadherins are a known earthly family of molecules, and zinc finger genes are a known earthly family of genes. This study reinforces the concept of common ancestry.

Do I need to add that it’s even plainly said in the abstract? Just read the abstract!

The core developmental and neuronal gene repertoire of the octopus is broadly similar to that found across invertebrate bilaterians

I just know this nonsense is going to be propagated by creationists everywhere, and I’m going to have to slam it down repeatedly. The only good thing is that it’s an easy one to rebut, and I’ll have many excuses to wrap my virtual tentacles around their rhetorical throats and squeeze.

Proving that octopuses are creatures that arrived from another planet, possibly from another solar system, may not be revealed any time soon. However, their alien existence upon the Earth is expected to be the focus of significant research in the coming years. It is likely that they will be found to be born of the Earth, but the mysticism that they may be aliens makes the genome discovery quite intriguing.

Abstract
Adult common octopus individuals were intramuscularly infected with Photobacterium damsela subsp. piscicida in order to investigate if this species is sensitive to this common and important fish pathogen. The fate of the bacterial antigens and the tissue responses of Octopus vulgaris were studied employing immunohistochemical techniques.

Strong reaction at the site of injection was evident from day 2 post-infection that continued until day 14. Great numbers of hemocytes that were attracted at the site of infection were involved in phagocytosis of bacteria. Very early in the infection, a transition of cells to fibroblasts and an effort to isolate the infection was observed. During the course of the study, very large necrotic cells were seen at the site of infection, whereas during the later stages hemocytes with phagocytosed bacteria were observed in well-defined pockets inside the muscle tissue. None of the internal organs tested for the presence of the bacterium were positive with the exception of the digestive gland where antigen staining was observed which was not associated with hemocyte infiltration. The high doses of bacterial cells used in this experimental infection and the lack of disease signs from Octopus vulgaris suggest that, under normal conditions, octopus is resistant to Photobacterium damsela subsp. piscicida.

Abstract
In recent decades, cephalopods have been shown to have very high capacities to accumulate most trace elements, regardless of whether they are essential (e.g., Cu and Zn) or non-essential (e.g., Ag and Cd). Among the different pathways of exposure to trace elements, the trophic pathway appears to be the major route of assimilation for numerous metals, including Cd, Co, Hg and Zn. Once assimilated, trace elements are distributed in the organism, accumulating in storage organs. The digestive gland is the main organ in which many trace elements accumulate, whichever of the exposure pathway. For example, this organ can present Cd concentrations reaching hundreds to thousands of ppm for some species, even though the digestive gland represents only a small proportion of the total mass of the animal. Such a specific organotropism towards the digestive gland of both essential and non-essential elements, regardless of the exposure pathway, poses the question of the detoxification processes evolved by cephalopods in order to sustain these high concentrations. This paper reviews the current knowledge on the bioaccumulation of trace elements in cephalopods, the differences in pharmaco-dynamics between organs and tissues, and the detoxification processes they use to counteract trace element toxicity. A peculiar focus has been done on the bioaccumulation within the digestive gland by investigating the subcellular locations of trace elements and their protein ligands.

1. Introduction
Cephalopods have been regarded as promising candidates for the diversification of marine aquaculture due to their great commercial interest [1]. Despite significant progress made over the last decade, culture of cephalopod species with pelagic paralarval stages like the common octopus Octopus vulgaris is still challenging due to the massive mortalities occurring upon the settlement phase [2]. The specific factors causing such mortalities of paralarvae remain unclear, although it has become increasingly obvious that nutritional issues associated with inadequate supply of essential nutrients such as lipids are crucial to ensure normal growth and development of O. vulgaris paralarvae and ultimately improve their viability [3].

Abstract
Regeneration is a process that restores structure and function of tissues damaged by injury or disease. In mammals complete regeneration is often unsuccessful, while most of the low phyla animals can re-grow many parts of their body after amputation. Cephalopod molluscs, and in particular Octopus vulgaris, are well known for their capacity to regenerate their arms and other body parts, including central and peripheral nervous system. To better understand the mechanism of recovery following nerve injury in this species we investigated the process of axon regrowth and nerve regeneration after complete transection of the Octopus pallial nerves. This injury induces scar formation and activates the proliferation of hemocytes which invade the lesion site. Hemocytes appear involved in debris removal and seem to produce factors that foster axon re-growth. Connective tissue is involved in driving regenerating fibers in a single direction, outlining for them a well-defined pathway. Injured axons are able to quickly re-grow thus to restoring structure and function.